data_3VT9
#
_model_server_result.job_id            sWi2uW4QkKw5kbait_bfQQ 
_model_server_result.datetime_utc      '2024-10-11 13:25:33' 
_model_server_result.server_version    0.9.12 
_model_server_result.query_name        ligand 
_model_server_result.source_id         pdb-bcif 
_model_server_result.entry_id          3vt9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":500}' 
#
_entry.id    3VT9 
#
_exptl.entry_id    3VT9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              486.726 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          95.63 
_cell.angle_gamma         90 
_cell.entry_id            3VT9 
_cell.length_a            154.714 
_cell.length_b            42.05 
_cell.length_c            41.972 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VT9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 software_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E 1 1 
A,C,D 2 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C31 H50 O4' 
_chem_comp.formula_weight    486.726 
_chem_comp.id                YI4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (1R,2Z,3R,5E,7E,9beta,17beta)-2-(2-hydroxyethylidene)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9-(prop-2-en-1-yl)-9,10-secoestra-5,7-diene-1,3-diol 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
O04 C33 YI4 sing 376 n n 
C33 C32 YI4 sing 377 n n 
C32 C02 YI4 doub 378 z n 
O01 C01 YI4 sing 379 n n 
C02 C01 YI4 sing 380 n n 
C02 C03 YI4 sing 381 n n 
C01 C10 YI4 sing 382 n n 
C03 O02 YI4 sing 383 n n 
C03 C04 YI4 sing 384 n n 
C10 C05 YI4 sing 385 n n 
C04 C05 YI4 sing 386 n n 
C05 C06 YI4 doub 387 z n 
C06 C07 YI4 sing 388 n n 
C07 C08 YI4 doub 389 e n 
C15 C14 YI4 sing 390 n n 
C15 C16 YI4 sing 391 n n 
C08 C14 YI4 sing 392 n n 
C08 C09 YI4 sing 393 n n 
C14 C13 YI4 sing 394 n n 
C18 C13 YI4 sing 395 n n 
C16 C17 YI4 sing 396 n n 
C09 C28 YI4 sing 397 n n 
C09 C11 YI4 sing 398 n n 
C28 C29 YI4 sing 399 n n 
C13 C17 YI4 sing 400 n n 
C13 C12 YI4 sing 401 n n 
C27 C25 YI4 sing 402 n n 
C29 C30 YI4 doub 403 n n 
C17 C20 YI4 sing 404 n n 
C24 C25 YI4 sing 405 n n 
C24 C23 YI4 sing 406 n n 
C11 C12 YI4 sing 407 n n 
C22 C23 YI4 sing 408 n n 
C22 C20 YI4 sing 409 n n 
C25 O03 YI4 sing 410 n n 
C25 C26 YI4 sing 411 n n 
C20 C21 YI4 sing 412 n n 
O03 H1 YI4 sing 413 n n 
C26 H2 YI4 sing 414 n n 
C26 H3 YI4 sing 415 n n 
C26 H4 YI4 sing 416 n n 
C27 H5 YI4 sing 417 n n 
C27 H6 YI4 sing 418 n n 
C27 H7 YI4 sing 419 n n 
C24 H8 YI4 sing 420 n n 
C24 H9 YI4 sing 421 n n 
C23 H10 YI4 sing 422 n n 
C23 H11 YI4 sing 423 n n 
C22 H12 YI4 sing 424 n n 
C22 H13 YI4 sing 425 n n 
C20 H14 YI4 sing 426 n n 
C21 H15 YI4 sing 427 n n 
C21 H16 YI4 sing 428 n n 
C21 H17 YI4 sing 429 n n 
C17 H18 YI4 sing 430 n n 
C16 H19 YI4 sing 431 n n 
C16 H20 YI4 sing 432 n n 
C15 H21 YI4 sing 433 n n 
C15 H22 YI4 sing 434 n n 
C14 H23 YI4 sing 435 n n 
C18 H24 YI4 sing 436 n n 
C18 H25 YI4 sing 437 n n 
C18 H26 YI4 sing 438 n n 
C12 H27 YI4 sing 439 n n 
C12 H28 YI4 sing 440 n n 
C11 H29 YI4 sing 441 n n 
C11 H30 YI4 sing 442 n n 
C09 H31 YI4 sing 443 n n 
C28 H32 YI4 sing 444 n n 
C28 H33 YI4 sing 445 n n 
C29 H35 YI4 sing 446 n n 
C30 H36 YI4 sing 447 n n 
C30 H37 YI4 sing 448 n n 
C07 H39 YI4 sing 449 n n 
C06 H40 YI4 sing 450 n n 
C10 H41 YI4 sing 451 n n 
C10 H42 YI4 sing 452 n n 
C01 H43 YI4 sing 453 n n 
O01 H44 YI4 sing 454 n n 
C04 H45 YI4 sing 455 n n 
C04 H46 YI4 sing 456 n n 
C03 H47 YI4 sing 457 n n 
O02 H48 YI4 sing 458 n n 
C32 H49 YI4 sing 459 n n 
C33 H50 YI4 sing 460 n n 
C33 H51 YI4 sing 461 n n 
O04 H52 YI4 sing 462 n n 
#
_atom_sites.entry_id                     3VT9 
_atom_sites.fract_transf_matrix[1][1]    0.006464 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000637 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023781 
_atom_sites.fract_transf_matrix[2][3]    0 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.023941 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
loop_
_pdbx_nonpoly_scheme.asym_id
_pdbx_nonpoly_scheme.entity_id
_pdbx_nonpoly_scheme.mon_id
_pdbx_nonpoly_scheme.pdb_strand_id
_pdbx_nonpoly_scheme.ndb_seq_num
_pdbx_nonpoly_scheme.pdb_seq_num
_pdbx_nonpoly_scheme.auth_seq_num
_pdbx_nonpoly_scheme.pdb_mon_id
_pdbx_nonpoly_scheme.auth_mon_id
_pdbx_nonpoly_scheme.pdb_ins_code
C 3 YI4 A 1 500 500 YI4 YI4 . 
D 4 HOH A 1 601 1 HOH HOH . 
D 4 HOH A 2 602 2 HOH HOH . 
D 4 HOH A 3 603 3 HOH HOH . 
D 4 HOH A 4 604 4 HOH HOH . 
D 4 HOH A 5 605 5 HOH HOH . 
D 4 HOH A 6 606 6 HOH HOH . 
D 4 HOH A 7 607 7 HOH HOH . 
D 4 HOH A 8 608 8 HOH HOH . 
D 4 HOH A 9 609 9 HOH HOH . 
D 4 HOH A 10 610 10 HOH HOH . 
D 4 HOH A 11 611 11 HOH HOH . 
D 4 HOH A 12 612 12 HOH HOH . 
D 4 HOH A 13 613 13 HOH HOH . 
D 4 HOH A 14 614 14 HOH HOH . 
D 4 HOH A 15 615 15 HOH HOH . 
D 4 HOH A 16 616 16 HOH HOH . 
D 4 HOH A 17 617 17 HOH HOH . 
D 4 HOH A 18 618 19 HOH HOH . 
D 4 HOH A 19 619 20 HOH HOH . 
D 4 HOH A 20 620 21 HOH HOH . 
D 4 HOH A 21 621 22 HOH HOH . 
D 4 HOH A 22 622 23 HOH HOH . 
D 4 HOH A 23 623 24 HOH HOH . 
D 4 HOH A 24 624 25 HOH HOH . 
D 4 HOH A 25 625 26 HOH HOH . 
D 4 HOH A 26 626 27 HOH HOH . 
D 4 HOH A 27 627 28 HOH HOH . 
D 4 HOH A 28 628 29 HOH HOH . 
D 4 HOH A 29 629 30 HOH HOH . 
D 4 HOH A 30 630 31 HOH HOH . 
D 4 HOH A 31 631 32 HOH HOH . 
D 4 HOH A 32 632 33 HOH HOH . 
D 4 HOH A 33 633 34 HOH HOH . 
D 4 HOH A 34 634 35 HOH HOH . 
D 4 HOH A 35 635 36 HOH HOH . 
D 4 HOH A 36 636 37 HOH HOH . 
D 4 HOH A 37 637 38 HOH HOH . 
D 4 HOH A 38 638 39 HOH HOH . 
E 4 HOH C 1 701 18 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 O O03 YI4 . . . C 3 9.54 -0.953 28.451 1 33.58 ? O03 YI4 500 A 1 
HETATM 2 C C25 YI4 . . . C 3 8.813 -0.029 27.636 1 30.78 ? C25 YI4 500 A 1 
HETATM 3 C C26 YI4 . . . C 3 7.913 0.805 28.562 1 29.31 ? C26 YI4 500 A 1 
HETATM 4 C C27 YI4 . . . C 3 7.964 -0.821 26.636 1 29.39 ? C27 YI4 500 A 1 
HETATM 5 C C24 YI4 . . . C 3 9.865 0.832 26.919 1 28.36 ? C24 YI4 500 A 1 
HETATM 6 C C23 YI4 . . . C 3 10.922 1.585 27.767 1 31.5 ? C23 YI4 500 A 1 
HETATM 7 C C22 YI4 . . . C 3 12.279 1.668 27.061 1 29.95 ? C22 YI4 500 A 1 
HETATM 8 C C20 YI4 . . . C 3 13.272 2.596 27.788 1 28.82 ? C20 YI4 500 A 1 
HETATM 9 C C21 YI4 . . . C 3 14.124 1.695 28.698 1 28.97 ? C21 YI4 500 A 1 
HETATM 10 C C17 YI4 . . . C 3 14.144 3.489 26.817 1 28.21 ? C17 YI4 500 A 1 
HETATM 11 C C16 YI4 . . . C 3 14.598 2.759 25.521 1 25.99 ? C16 YI4 500 A 1 
HETATM 12 C C15 YI4 . . . C 3 15.079 3.856 24.553 1 28.02 ? C15 YI4 500 A 1 
HETATM 13 C C14 YI4 . . . C 3 14.926 5.108 25.433 1 30.84 ? C14 YI4 500 A 1 
HETATM 14 C C13 YI4 . . . C 3 13.655 4.876 26.268 1 29.76 ? C13 YI4 500 A 1 
HETATM 15 C C18 YI4 . . . C 3 12.269 4.828 25.488 1 24.8 ? C18 YI4 500 A 1 
HETATM 16 C C12 YI4 . . . C 3 13.504 5.971 27.352 1 28.93 ? C12 YI4 500 A 1 
HETATM 17 C C11 YI4 . . . C 3 13.736 7.466 26.966 1 30.17 ? C11 YI4 500 A 1 
HETATM 18 C C09 YI4 . . . C 3 14.633 7.778 25.704 1 35.31 ? C09 YI4 500 A 1 
HETATM 19 C C28 YI4 . . . C 3 15.975 8.404 26.187 1 38.71 ? C28 YI4 500 A 1 
HETATM 20 C C29 YI4 . . . C 3 16.925 7.548 26.776 1 45.21 ? C29 YI4 500 A 1 
HETATM 21 C C30 YI4 . . . C 3 17.905 8.061 27.615 1 47.01 ? C30 YI4 500 A 1 
HETATM 22 C C08 YI4 . . . C 3 14.778 6.53 24.715 1 31.16 ? C08 YI4 500 A 1 
HETATM 23 C C07 YI4 . . . C 3 14.757 6.659 23.315 1 28.11 ? C07 YI4 500 A 1 
HETATM 24 C C06 YI4 . . . C 3 14.626 7.775 22.475 1 23.53 ? C06 YI4 500 A 1 
HETATM 25 C C05 YI4 . . . C 3 14.31 7.907 21.118 1 27.08 ? C05 YI4 500 A 1 
HETATM 26 C C10 YI4 . . . C 3 14.014 6.708 20.171 1 23.4 ? C10 YI4 500 A 1 
HETATM 27 C C01 YI4 . . . C 3 14.646 6.858 18.766 1 22.21 ? C01 YI4 500 A 1 
HETATM 28 O O01 YI4 . . . C 3 14.071 5.892 17.887 1 20.33 ? O01 YI4 500 A 1 
HETATM 29 C C04 YI4 . . . C 3 14.25 9.336 20.532 1 25.52 ? C04 YI4 500 A 1 
HETATM 30 C C03 YI4 . . . C 3 14.934 9.451 19.155 1 27.38 ? C03 YI4 500 A 1 
HETATM 31 O O02 YI4 . . . C 3 16.346 9.395 19.402 1 29.14 ? O02 YI4 500 A 1 
HETATM 32 C C02 YI4 . . . C 3 14.436 8.317 18.216 1 26.89 ? C02 YI4 500 A 1 
HETATM 33 C C32 YI4 . . . C 3 13.831 8.467 16.95 1 31.46 ? C32 YI4 500 A 1 
HETATM 34 C C33 YI4 . . . C 3 13.506 9.593 16.181 1 32.75 ? C33 YI4 500 A 1 
HETATM 35 O O04 YI4 . . . C 3 12.621 9.233 15.126 1 47.2 ? O04 YI4 500 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           35 
#